Phylotranscriptomics reveals extensive gene duplication in the subtribe Gentianinae (Gentianaceae)
Phylotranscriptomics reveals extensive gene duplication in the subtribe Gentianinae (Gentianaceae)
复制标题
系统转录组学揭示龙胆亚族（龙胆科）中存在广泛的基因重复
DOI：
10.1111/jse.12651
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发表时间：
2020-07-27
影响因子：
3.7
通讯作者：
Xi, Zhen-Xiang
中科院分区：
文献类型：
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作者：
Chen, Chun-Lin;Zhang, Lei;Xi, Zhen-Xiang
基因复制在植物多样化和适应新生境中起着重要作用。我们对来自67个物种的70个转录组进行了测序和组装，这些转录组代表了龙胆亚族中所有6个已知属以及密切相关的外群。利用系统基因组学方法，龙胆科的骨干关系几乎完全解决了高bootstrap支持。虽然在核系统发生和质体系统发生之间观察到冲突的情况，但在两个系统发生中一致地恢复了龙胆科的六个主要分支。此外，我们发现在我们的转录组组装中重复基因的发生率很高。利用多种基因树和解方法，我们在物种树中共鉴定出10个重复基因浓度较高的节点。进一步分析表明，许多重复基因可能来自杂交多倍体，这也可能解释了龙胆科核与质体系统发育之间的一些拓扑不一致。
Gene duplication plays an important role in plants for diversification and adaptation to new habitats. In this study, we aim to reconstruct the genome-scale phylogeny and identify large-scale gene duplication events for the subtribe Gentianinae (Gentianaceae), which is a great symbol of the alpine plants in the Qinghai-Tibet Plateau. We sequenced and assembled 70 transcriptomes from 67 species, representing all six recognized genera in the subtribe Gentianinae plus the closely related outgroups. Using phylogenomic approaches, the backbone relationships of Gentianinae were almost fully resolved with high bootstrap support. Although instances of conflicts were observed between nuclear and plastid phylogenies, six major clades of Gentianinae were consistently recovered in both phylogenies. In addition, we revealed a high occurrence of duplicated genes in our transcriptome assemblies. Using several gene tree reconciliation methods, we collectively identified 10 nodes in the species tree with large concentrations of duplicated genes. Further analysis indicated that many of these duplicated genes likely arose from hybrid polyploidy, which might also account for some of the topological incongruences between nuclear and plastid phylogenies in Gentianinae.